Anyway, back to the problem. If you have 3% from 300 AA protein, that is only 6 amino acids, right? You cannot use that for identification. I bet that even the size doesn't fit. Try the N-term. sequencing, but that will not help that much. If you have enough of protein (and it's sufficiently clean), they should be able to sequence it using the MALDI-TOF.In any case, because you will probably not have the protein in any database, you will have to create some gDNA/cDNA library and use blotting with (degenerated) probe.

i have to find a facility where i can do N-term sequencing. we don't have it here.

i have abt 1.5mg of protein, ran on SDS-PAGE got a single band, but when i did 2DE i got 2 spots of the same MW but different pI. sent it for MALDI-ToF-ToF, this is the result i got. I was hoping that this protein would be a new protein.

I just wanted assurance to rule out the possibility of this being a preparation error.